In the Ontology of Craniofacial Development and Malformation (OCDM) [1] we created malformation ontologies for the human (Craniofacial Human Malformation Ontology [CHMO]), the mouse (Craniofacial Mouse Malformation Ontology [CMMO]) and the zebrafish (Craniofacial Zebrafish Malfomration Ontology [CZMO]) to comprehensively represent in all three species the different pathological entities involved in cranial dysmorphologies, and in particular, the phenotypic and genotypic abnormalities associated with craniofacial microsomias and their correlation to normal and canonical anatomical entities and their corresponding embryological development.